BMB 411 – READINGS IN BMB – 09/23/20 5
Paper: Chakrabortee, et al. (2016). "Intrinsically disordered proteins drive emergence
and inheritence of biological traits." Cell 167: 369-381 + optional “Preview”.
Please fashion preliminary answers to the following questions before our class meeting
on Wednesday 09/23/20 and email me your responses (rmyers@miami.edu); this will
help direct your reading of the paper. Write your answers directly into this PreDiscussion File following each question; do not modify the file in any other way. Save
your answers to a file named exactly like this:
Post-Discussion BMB 411 Fall 2020 Paper Five Katherine Mallol
(where YOUR NAME is “your name”…e.g. RIK MYERS)
Send this file as an attachment to rmyers@miami.edu with the following subject heading
(exactly as written below):
Post-Discussion BMB 411 Fall 2020 Paper Five
After the meeting on 09/23/20, revisit your answers and modify them to suit your
evolved understanding. Return these re-answered questions via email to
rmyers@miami.edu before 5 PM on Friday 09/25/20. Save the second set of answers
as before, except replace “Pre-Discussion” with “Post-Discussion”. Also send your email
with the subject as I said before except again replace “Pre-Discussion” with “PostDiscussion”. I want two sets of answers from you. If your understanding remains the
same after the discussion, submit your answers again with the appropriate change to
the file name. I use this information to see how your thinking is altered by the in-class
discussion.
Q1:
What is the overall hypothesis of the paper?
The overall hypothesis of this paper was to examine the protein based
inheritance of the yeast proteome by assessing every open reading frame that
induces heritable traits.
Q2:
In general terms, what is the plan Chakrabortee et al. came up with to
test their hypothesis in Q1? For example: Did they create mutants, knock-down
expression of a key gene and examine phenotypes, look for protein-protein
interactions, etc.
In general, Chakrabortee et al. tested their hypothesis by using prion like proteins
known to each induce different adaptive traits and phenotypes. They examined
phenotypes that the prions induced in commercial and wild type yeast strains and
then analyzed whether heritable traits were produced, if any, and if they were
favorable and adaptive, or unfavorable and maladaptive.
Q3:
What experimental techniques were used to carry out the plan in Q2?
Experimental techniques used to carry out the plan in Q2 was to propagate a
self-templating assembly mechanism, growing strains of yeast in a standard
medium to analyze what adaptive features were produced as a result from the
prion like proteins in yeast. Additionally, the authors screened the yeast
proteome for its ability to elicit stable biological traits through expression of ORF
and the gold standard test.
Q4:
Why did the authors choose to use both laboratory and commercial
yeast strains for these studies? What unique features led the investigators to use
this biological system? What experimental limits did this choice of material
create?
The authors chose to use both laboratory and commercial yeast strains for these
studies because each strain holds different adaptive qualities unique to the
strains. Yeast is a bacterium very easy to grow in the lab in large quantities and it
is not costly, which makes it highly favorable to use in in a study with various
experiments. Experimental limits this choice of material created was that
because they only investigated yeast and not other bacteria, this makes it difficult
to see the application in other eukaryotic bacteria or in live specimen such as
mice. Additionally, using yeast only permits them to investigate a handful of prion
-like proteins and that is not enough to demonstrate the degree of HSP104
independence.
Q5:
What were the overall conclusions from these studies?
The overall conclusions from these studies were that prion-based protein
inheritance drives the emergence of new phenotypic traits and have beneficial
adaptive properties depending on their inhibiting factor. For example, some of
these behaviors actually propagate evolution in the sense that it encourages the
beneficial traits for the yeast under stressful situations. This, in the long run,
produces cells with the same beneficial adaptative features.
Q6:
What topic or question do you think the authors will take up next based
on this paper? What are the important next questions raised?
A topic or question the authors will take up next based on this paper is how do
these prion-like proteins, if, and how they induce biological traits in a mice
specimen? A question this study raised is can we apply this study to induce
favorable biological traits in humans through proteins? Another question this
raises is how can this mechanism of phenotype inducing prions be used to alter
phenotypes in genetic engineering of animals and humans?
BMB 411 – READINGS IN BMB – 09/23/20 5
Q7:
Identify three different experiments that the authors used to come to the
conclusion you stated in answer to Question 5. State what you perceive to be a
limitation to one or more of these experiments that might weaken their
conclusions.
Three different experiments the authors used to come to the conclusion stated in
question five is the experiment in which they individually and systematically
overexpressed nearly every known ORF in S.Cerevisia from a single copy
plasmid with a galactose-inducible promoter and examined how this affected the
growth of the bacterium in ten different conditions. In a second experiment, the
authors examined whether transient HSP104 inhibition could eliminate traits
emerged in their screen. Finally, in a third experiment, the authors tested whether
HSP90 might influence any of the 16 heritable phenotype states by propagating
strains to harbor them four times in media containing radicicol, a potent HSP90
inhibitor. A limitation to the third experiment is that components of the protein
homeostasis machinery may influence the inheritance of the 14 remaining
phenotypic states.
Q8:
Chakrabortee et al. spend most of the paper investigating "prion-like"
proteins. How are these different from "regular" prions such as [PSI+]? How are
they the same? What conclusions do you think we can draw about prions like
[PSI+] from the data in the paper?
Prion like proteins are different from regular prions in the sense that they each
produce different heritable traits. Although the prion like proteins share the same
unusual patterns of inheritance as prions, but one not known to prions.
Additionally, the prions they discovered, resemble unique prion-like elements,
such as its adaptive values, an altered metabolic dynamic and most are HSP104
independent.
Q9:
It has been shown that for some prions, both loss of Hsp104
function and overexpression of Hsp104 can remove prion states from cells.
Given what you know about prions from Chakrabortee et al. and the information
on Hsp104 that can be found at uniprot.org, propose a mechanism of action for
Hsp104 that can predict the results of both its inactivity and hyperactivity.
A mechanism of action for HSP104 that can predict the results of both its
inactivity and hyperactivity would be to test with different prion like proteins that
are independent and dependent on HSP104 and analyze the activity in each of
these prion like proteins to determine what is causing the overdependency or
independency on HSP104 of these prions.
Q10:
In this paper Chakrabortee et al. attempt to find an adaptive (that is,
“selective” in the Darwinian evolution sense) function for prions. Some scientists
work under the assumption that all the events taking place in a cell are adaptive.
Is there good reason to hold this assumption; why or why not?
There is a good reason to hold this assumption that all events taking place in a
cell are adaptive because these cells are generated from cells that have
developed and adapted to their environment already which is why they were able
to generate cells that have these same favorable qualities. However, this
statement has another side to it and that side is that there are some events in
cells that are maladaptive, but these cells often don’t survive to regenerate more
of their kind because according to Darwin’s theory of natural selection, only those
who adapt and are physically “fit” for their surroundings survive to reproduce.